A novel and simple hydrophobicity scale derived from the Kyte-Doolittle hydrophobicity scale leads to a performance improvement of around 10% in ranking, cluster quality and water recovery at the interface compared with the statistics-based original solvated docking protocol.
This study performed mixed-solvent molecular dynamics simulations using four types of probe molecules to improve the accuracy of large-scale VS and proposed a method for the modification of the docking scoring function for five selected atom classifications (XS_types).
Kaho Akaki, Keisuke Yanagisawa, Yutaka Akiyama· Journal of Chemical Informat...· 0 citations
The explicit first solvation shell remains a pivotal challenge in quantum chemical studies of solution‐phase systems. A surface coverage‐based protocol to construct explicit solvation environment is presented, in which the number and arrangement of solvent molecules emerge from the percentage of Solvent Accessible Surf...
Yamil Hernández‐Urquieta, Andrea Moreno-Ceballos, M. Castro et al.· Journal of Computational Che...· 0 citations
HydroDock is extended to challenging targets with open binding pockets, populated by highly mobile water molecules that are the most troublesome for drug design, and improved docking accuracy with increases of 28% (10%) in median structural (and ranking) performance.
Bayar Bayarsaikhan, C. Hetényi, B. Z. Zsidó· ACS Physical Chemistry Au· 0 citations
Amino acid behavior in water-mediated processes is not well captured by hydrophobicity or side-chain class alone, because residues with similar hydropathy can differ in charge localization, geometry, surface exposure, and hydration response. The objective of this study is to determine whether integrating complementary...
Yusung Ok, Youngjune Park· Journal of Chemical Informat...· 0 citations
In quantum chemical descriptions of solutions, solvents are treated either implicitly, accounting only for bulk properties, or explicitly by including solvent molecules in the calculations. Although explicit treatments are more accurate, they are often computationally prohibitive. As a cost-effective alternative, micro...
Lukas Magenheim, Maren Podewitz· Journal of Chemical Theory a...· 0 citations
ChalcoVina is presented, an augmented molecular docking program based on AutoDock Vina that simultaneously evaluates intermolecular and intramolecular ChBs for the first time and can be a blueprint for other σ-hole-mediated interactions, facilitating the inclusion of more nonclassical interactions in SBDD.
Wen-Hao Cai, Zi-Yue Li, Yi-Jie Wang et al.· Journal of Chemical Informat...· 0 citations
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